This code provides examples of visualizations that could eventually be shown on MERMAID Explore for a macroinvertebrate protocol. This protocol has not been added yet but is in progress.
Getting summary sample event data from MERMAID
Since the protocol hasn’t actually been added yet, this section loads data from a local mock-up file.
Once the protocol is added, this section can be updated to download summary sample event data from MERMAID, using the mermaidr package (documentation can be found at https://data-mermaid.github.io/mermaidr/).
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rm(list =ls()) #remove past stored objectsoptions(scipen =999) #turn off scientific notation# ### Load packages and libraries ##### # If this is the first time using mermaidr, install the package through "remotes"# install.packages("remotes")# remotes::install_github("data-mermaid/mermaidr")# install.packages("tidyverse")# install.packages("plotly")# install.packages("htmlwidgets")library(mermaidr) #package to download data from datamermaid.orglibrary(tidyverse) #package that makes it easier to work with datalibrary(plotly) #for interactive plottinglibrary(htmlwidgets) #for saving plots at html fileslibrary(readxl)## Get mock-up data from local XLSX filemacroinvertbeltSurveySummTBL <-read_excel("../data/[mermaidr mockup] Macroinvertebrates belt - Dummy data.xlsx",sheet ="sampleevents")#### This next section is what could eventually be used for summary sample events# #### Get data from MERMAID for creating aggregate visualizations ##### allMermaidSampEventsTBL <- mermaidr::mermaid_get_summary_sampleevents()
Histogram - Macroinvertebrate densities from sample events
This code creates a histogram of the macroinvertebrate density data from the sample events available. Currently this uses the sample events from the mock-up data but eventually could run on all projects with permissions of “public summary” or “public” using the summary sample events MERMAID endpoint. It includes the total number of surveys (i.e. sample events in MERMAID).
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### Macroinvertebrate density data - only use relevant data### optionally truncate > 5000 ind/ha# macroinvertbeltSurveySummTBL <- allMermaidSampEventsTBL %>%# filter(!is.na(density_indha_avg)) %>%# mutate(truncDensity = ifelse(test = density_indha_avg > 5000,# yes = 5001,# no = density_indha_avg))# Calculate dynamic tick valuesmax_density <-max(macroinvertbeltSurveySummTBL$density_indha_avg, na.rm =TRUE)# Determine rounding interval based on max valueif (max_density <=1000) { interval <-100 max_tick <-ceiling(max_density /100) *100} else { interval <-1000 max_tick <-ceiling(max_density /1000) *1000}# Create sequence of tick values - centered on binstick_vals <-seq(interval/2, max_tick + interval/2, by = interval) # Include one more bintick_text <-as.character(seq(0, max_tick, by = interval)) # Labels from 0 to max_tick# Add "+" to the last ticktick_text[length(tick_text)] <-paste0(tick_text[length(tick_text)], "+")### Create the plotmacroinvertbeltAggHist <-plot_ly(data = macroinvertbeltSurveySummTBL,x =~density_indha_avg,type ='histogram',xbins =list(start =0, size =100),marker =list(color ="#769fca"),height =450,hovertemplate =paste('Bin: %{x} ind/ha','<br>%{y} surveys','<extra></extra>')) %>%config(displayModeBar =TRUE,displaylogo =FALSE,modeBarButtonsToRemove =c('zoom','pan', 'select', 'zoomIn', 'zoomOut','autoScale', 'resetScale', 'lasso2d','hoverClosestCartesian', 'hoverCompareCartesian')) %>%layout(bargap =0.1,xaxis =list(title ="Macroinvertebrate density (ind/ha)",range =c(0, max_tick + interval),linecolor ="black",linewidth =2,tickmode ="array",ticktext = tick_text,tickvals = tick_vals),yaxis =list(title ="Number of surveys",linecolor ="black",linewidth =2),annotations =list(list(x =0, y =1.15,text ="MACROINVERTEBRATE DENSITY", showarrow =FALSE, xref ='paper', yref ='paper', xanchor ='left', yanchor ='top',font =list(size =20)),list(x =0, y =1.08,text =paste0(length(macroinvertbeltSurveySummTBL$density_indha_avg)," Surveys"),showarrow =FALSE, xref ='paper', yref ='paper', xanchor ='left', yanchor ='top',font =list(size =12)) ),margin =list(t =50, b =75))# Visualize the plotmacroinvertbeltAggHist
Time series - Densities by year and management
Barplots showing the average macroinvertebrate density (y-axis), each year (x-axis), separately for open access fisheries restricted areas (open access = green, restrictions = blue).
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## Assign either "Open Access" or "Restrictions" to macroinvertebrate management macroinvertSurveyManagementTBL <- macroinvertbeltSurveySummTBL %>%filter(!is.na(density_indha_avg)) %>%mutate(open_access =case_when(management_rules =="open access"~"Open Access",.default ="Restrictions"),open_access =factor(open_access,levels =c("Restrictions", "Open Access")))## Summarize to get the density by year and management (open access vs restricted)macroinvertbeltDensityByYearManagementTBL <- macroinvertSurveyManagementTBL %>%mutate(year =year(sample_date)) %>%group_by(year, open_access) %>% dplyr::summarise(MeanMacroinvertDensity =mean(density_indha_avg),.groups ="keep") managementColorMap <-setNames(object =c("#E69F00", "#70AAE6"),nm =c("Open Access", "Restrictions"))macroinvertbeltTimeSeriesBarplot <-plot_ly(data = macroinvertbeltDensityByYearManagementTBL,x =~year,y =~MeanMacroinvertDensity,color =~open_access,colors = managementColorMap,type ='bar',hovertemplate =paste('%{fullData.name}','<br>Year: %{x}','<br>%{y:.0f} ind/ha','<extra></extra>'),height =450) %>%config(displayModeBar =TRUE,displaylogo =FALSE,modeBarButtonsToRemove =c('zoom','pan', 'select', 'zoomIn', 'zoomOut','autoScale', 'resetScale', 'lasso2d','hoverClosestCartesian','hoverCompareCartesian')) %>%layout(bargap =0.1,xaxis =list(title ="Year",linecolor ="black",linewidth =2,dtick =1, # Add this: tick every 1 yeartick0 =min(macroinvertbeltDensityByYearManagementTBL$year)), # Add this: start at first yearyaxis =list(title ="Macroinvertebrate density (ind/ha)",linecolor ="black",linewidth =2),annotations =list(list(x =0, y =1.15, text ="MACROINVERTEBRATE DENSITY", showarrow =FALSE, xref ='paper', yref ='paper', xanchor ='left', yanchor ='top',font =list(size =20)),list(x =0, y =1.08,text =paste(length(macroinvertSurveyManagementTBL$density_indha_avg)," Surveys"),showarrow =FALSE, xref ='paper', yref ='paper', xanchor ='left', yanchor ='top',font =list(size =12)) ),legend =list(orientation ="h", xanchor ="center", x =0.5, y =-0.2),margin =list(t =50, b =75))# Visualize the plotmacroinvertbeltTimeSeriesBarplot
Barplot - Densities by trophic group (single survey)
Barplot showing macroinvertebrate densities (y-axis) by trophic group (x-axis, with different colors for each group). This is an example with a single sample event (i.e. survey), but the code could easily be adapted to show averages across surveys or sites.
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## Get a single sample event that has density in each of the groups of interest as an examplemacroinvertbeltSingleSeTBL <- macroinvertbeltSurveySummTBL %>%filter(density_indha_avg >0) %>%select(starts_with("density_indha_group_interest_avg"), sample_unit_count) %>%select(-density_indha_group_interest_avg_other) %>%#remove "Other"replace(is.na(.), 0) #replace NA's with zeroes## Define exact label mappinginterestLabelMap <-c("conchs"="Conchs","crabsshrimps"="Crabs / Shrimps","cots"="COTS","corallivoroussnails"="Corallivorous snails","giantclams"="Giant clams","lobsters"="Lobsters","octopus"="Octopus","pearloysters"="Pearl oysters","polychaeteworms"="Polychaete worms","seacucumbers"="Sea cucumbers","seaurchins"="Sea urchins","tritonstrumpets"="Triton's trumpets","trochusshells"="Trochus shells","turbanshells"="Turban shells")## create fixed label and color mapping for the trophic levelsinterestLabels_raw <-gsub(x =colnames(macroinvertbeltSingleSeTBL %>%select(-sample_unit_count)),pattern ="density_indha_group_interest_avg_",replacement ="")## Apply mapping to get pretty labelsinterestLabels <- interestLabelMap[interestLabels_raw]names(interestLabels) <-NULLinterestColorMap <-setNames(object =c( "#E69F00","#56B4E9","#009E73","#F0E442","#0072B2","#D55E00","#CC79A7","#999999","#117733","#882255","#44AA99","#AA4499","#332288","#DDCC77"),nm = interestLabels)## Remove zero values before plottinginterestCols <-colnames(macroinvertbeltSingleSeTBL %>%select(-sample_unit_count))values_all <-as.numeric(unlist(macroinvertbeltSingleSeTBL[1, interestCols], use.names =FALSE))keep <- values_all !=0interestLabels_plot <-as.character(interestLabels[keep])values_plot <- values_all[keep]# drop unused categoriesinterestLabels_plot <-factor(interestLabels_plot, levels = interestLabels_plot)## Plot macroinvertebrate density by group of interest macroinvertbeltSingleSeBarplot <-plot_ly(x = interestLabels_plot,y = values_plot,type ="bar",color = interestLabels_plot,colors = interestColorMap[as.character(interestLabels_plot)],marker =list(line =list(color ="black", width =1)),hovertemplate =paste('%{x}','<br>%{y:.1f} ind/ha','<extra></extra>'),height =450) %>%config(displayModeBar =TRUE,displaylogo =FALSE,modeBarButtonsToRemove =c('zoom','pan', 'select', 'zoomIn', 'zoomOut','autoScale', 'resetScale', 'lasso2d','hoverClosestCartesian','hoverCompareCartesian')) %>%layout(showlegend =FALSE,bargap =0.1,xaxis =list(title ="Group of interest",linecolor ="black",linewidth =2, tickangle =-45),yaxis =list(title ="Macroinvertebrate density (ind/ha)",linecolor ="black", # Set the y-axis line color to blacklinewidth =2),annotations =list(list(x =0, y =1.15, text ="MACROINVERTEBRATE DENSITY", showarrow =FALSE, xref ='paper', yref ='paper', xanchor ='left', yanchor ='top',font =list(size =20)),list(x =0, y =1.07,text =paste0(macroinvertbeltSingleSeTBL$sample_unit_count[1]," sample units"),showarrow =FALSE, xref ='paper', yref ='paper', xanchor ='left', yanchor ='top',font =list(size =12)) ),margin =list(t =50, b =75)) # Increase top margin to create more space for title and subtitle# Visualize the plotmacroinvertbeltSingleSeBarplot
